Hi again Massimo, please, show me as well what you have in your targets$GErep p.- On Mon, Apr 27, 2009 at 4:01 PM, Pedro Lopez-Romero < plromero1.bioc@gmail.com> wrote: > Hi Massimo, can you show me what you have in targets$Treatment? > > p.- > > On Mon, Apr 27, 2009 at 7:17 AM, Massimo Pinto wrote: > >> I am reposting this only because, from the web archive of this list, it >> appears that >> An embedded and charset-unspecified text was scrubbed... >> Name: not available >> >> So perhaps my message was never seen on the list, but for those who opt to >> receive individual message. Thank you. >> Massimo >> >> ---------- Forwarded message ---------- >> From: Massimo Pinto >> Date: Fri, Apr 24, 2009 at 6:02 PM >> Subject: Agi4x44PreProcess: filtration of probes using filter.probes() >> returns an empty RGList. >> To: bioconductor@stat.math.ethz.ch >> >> >> Greetings, >> on a BioC2.4 installation using with the Agi4x44PreProcess library, I am >> trying to invoke the filter.probes() filtration function to remove those >> not-so-good probes. >> Keeping in mind that my object looks like this: >> > dim(ddNORM) >> [1] 45015 4 >> > class(ddNORM) >> [1] "RGList" >> attr(,"package") >> [1] "limma" >> >> when I apply the filtration function at the R prompt, using a syntax that >> I >> am copying from the Agi4x44PreProcess manual: >> >> >ddFILT = filter.probes(ddNORM, control = TRUE, wellaboveBG = TRUE, >> isfound >> = TRUE, wellaboveNEG = TRUE, sat = TRUE, PopnOL = TRUE, NonUnifOL = T, nas >> = >> TRUE, limWellAbove = 75, limISF = 75, limNEG = 75, limSAT = 75, limPopnOL >> = >> 75, limNonUnifOL = 75, limNAS = 100, makePLOT = TRUE, annotation.package = >> "hgug4112a.db", flag.counts = T, targets) >> I am getting an empty RGList as output: >> FILTERING BY ControlType FLAG >> ------------------------------------------------------ >> PROBES BEFORE FILTERING: 45015 >> PROBES AFTER ControlType FILTERING: 43376 >> RAW DATA WITHOUT CONTROLS OUT : 43376 >> ------------------------------------------------------ >> FILTERING BY IsWellAboveBG filterFLAG >> FLAG FILTERING OPTIONS - FLAG OK = 1 - limWellAbove: 75 % >> PROBES BEFORE FILTERING: 43376 >> PROBES AFTER QC FILTERING: 0 >> IsNOTWellAboveBG OUT : 0 >> ------------------------------------------------------ >> [...] >> so it looks to me like filtration by ControlType flag works ok, but >> filtration via filter flag IsWellAboveBG returns an empty RGlist, which >> remains empty from there onwards, as it seems: >> > dim(ddFILT) >> [1] 0 4 >> However, looking into the variable IsWellAboveBG somewhere in my RGList >> ddNORM returns >> > ddNORM$other$gIsWellAboveBG[8165:8178,] >> 41745_1_3_21 41844_1_2_22 41744_1_2_23 41743_1_3_24 >> [1,] 1 1 1 1 >> [2,] 1 1 1 1 >> [3,] 0 0 0 0 >> [4,] 0 0 0 0 >> [5,] 1 1 1 1 >> [6,] 0 0 0 0 >> [7,] 1 1 1 1 >> [8,] 1 1 1 1 >> [9,] 1 1 1 1 >> [10,] 0 0 0 0 >> [11,] 0 0 0 0 >> [12,] 1 1 1 1 >> [13,] 1 1 1 1 >> [14,] 1 1 1 1 >> >> suggesting that, in ddNORM, does have some entries have value 1 for flag >> IsWellAboveBG. So why is filter.probes() throwing out all of my data from >> ddNORM, assuming none is above background? >> I have also tried to suppress filtation by IsWellAboveBG, but the outcome >> is >> the same upon the next filtration invoked by filter.probes(), i.e. an >> empty >> RGList. >> Thank you very much indeed for any clues you may have. Clearly I cannot >> see >> clearly in the use of this function. >> Yours >> Massimo >> >> Massimo Pinto >> Post Doctoral Research Fellow >> Enrico Fermi Centre and Italian Public Health Research Institute (ISS), >> Rome >> http://claimid.com/massimopinto >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]